Prediction of transition metal-binding sites from apo protein structures

Mariana Babor, Sergey Gerzon, Barak Raveh, Vladimir Sobolev*, Marvin Edelman

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

107 Scopus citations

Abstract

Metal ions are crucial for protein function. They participate in enzyme catalysis, play regulatory roles, and help maintain protein structure. Current took for predicting metal-protein interactions are based on proteins crystallized with their metal ions present (holo forms). However, a majority of resolved structures are free of metal ions (apo forms). Moreover, metal binding is a dynamic process, often involving conformational rearrangement of the binding pocket. Thus, effective predictions need to be based on the structure of the apo state. Here, we report an approach that identifies transition metal-binding sites in apo forms with a resulting selectivity >95%. Applying the approach to apo forms in the Protein Data Bank and structural genomics initiative identifies a large number of previously unknown, putative metal-binding sites, and their amino acid residues, in some cases providing a first clue to the function of the protein.

Original languageAmerican English
Pages (from-to)208-217
Number of pages10
JournalProteins: Structure, Function and Genetics
Volume70
Issue number1
DOIs
StatePublished - Jan 2008
Externally publishedYes

Keywords

  • Molecular modeling
  • Protein function
  • Structural bioinformatics
  • Structural genomics
  • Structure prediction

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